exprSetRG-class          package:arrayMagic          R Documentation

_C_l_a_s_s _e_x_p_r_S_e_t_R_G _f_o_r _t_w_o _c_o_l_o_u_r _D_N_A _m_i_c_r_o_a_r_r_a_y _d_a_t_a
(_e_x_t_e_n_s_i_o_n _o_f _e_x_p_r_S_e_t)

_D_e_s_c_r_i_p_t_i_o_n:

     This is a class representation for two colour DNA microarray data.
     The class is based on the class 'exprSet' of the 'Biobase'
     package. The red and green channels  are stored in a single
     'exprSet' object. The information on the corresponding red-green
     pairs is stored separately. Several class methods offer a
     convienent way to access and set data.

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     '  new('exprSetRG','
      '    channels = ..., # object of class matrix with columns
     "green" and "red" '
      '    exprs    = ..., # object of class matrix'
      '    se.exprs = ..., # object of class matrix'
      '    phenoData= ..., # object of class phenoData'
      '    notes    = ..., # object of class character'
      '    annotation    = ..., # object of class character'
      '  )'

_S_l_o_t_s:

     '_i_n_d_G_r_e_e_n': Object of class 'vector'; indexes of the green channel

     '_i_n_d_R_e_d': Object of class 'vector'; indexes of the red channel

     '_e_x_p_r_s': Object of class 'matrix'; the observed expression levels.
          This is a matrix with columns representing the red and green
          channels and rows representing genes. Each row in 'channels'
          lists the indexes of the corresponding pair of red and green
          channels representing a single microarray slide.

     '_s_e._e_x_p_r_s': Object of class 'matrix'; this is a matrix of the same
          dimensions as 'exprs', e.g. useful to represent the standard
          error estimates for the corresponding expression levels. 

     '_p_h_e_n_o_D_a_t_a': Object of class 'phenoData', i.e. an instance of
          class 'phenoData'  containing annotation information on the
          individual channels. The columns of the pData slot of this
          entity represent variables and the rows represent channels. 

     '_n_o_t_e_s': Object of class 'character' containing explanatory text;
          default: ""

     '_a_n_n_o_t_a_t_i_o_n': Object of class 'character'; default: ""

_E_x_t_e_n_d_s:

     Class 'exprSet', directly.

_M_e_t_h_o_d_s:


     _s_h_o_w (exprSetRG): renders information about the exprSetRG in a
          concise way on stdout, cf. class exprSet.

     _g_e_t_E_x_p_r_S_e_t_L_o_g_R_a_t_i_o (exprSetRG, seExprsHandling): Returns an
          'exprSet' object of the difference of the expression levels,
          i.e. the green channel minus the red channel.  The
          'phenoData' slot it the result of calling the class method
          'phenoDataSlide' on the object 'exprSetRG'. The 'se.exprs'
          slot contains the root-mean-square or the mean of the
          se.exprs of both channels depending on the argument
          'seExprsHandling'. The root-mean-square might be useful if
          the two se.exprs values are estimated standard deviations
          based on the same number observations and identical
          distribution. 'seExprsHandling' must be a character string;
          possible values are "rootMeanSquare" or "mean"; the default
          value is "rootMeanSquare". 

     _g_e_t_E_x_p_r_S_e_t_G_r_e_e_n_M_i_n_u_s_R_e_d same as method 'getExprSetLogRatio' 

     _g_e_t_E_x_p_r_S_e_t_R_e_d_M_i_n_u_s_G_r_e_e_n similar to method 'getExprSetLogRatio';
          the "negative" difference of the expression levels is
          returned, i.e. the red channel minus the green channel.


     _g_e_t_E_x_p_r_S_e_t_G_r_e_e_n (exprSetRG): Returns an 'exprSet' object which
          contains the expression levels of the green channel and the
          corresponding annotation.

     _g_e_t_E_x_p_r_S_e_t_R_e_d (exprSetRG): Returns an 'exprSet' object which
          contains the expression levels of the red channel and the
          corresponding annotation.

     _p_h_e_n_o_D_a_t_a_S_l_i_d_e (exprSetRG): Returns an 'phenoData' object
          characterizing all microarray slides. Those annotation
          information, which is the same for both channels (and not
          'NA') is taken directly, e.g. the the slide number. All other
          annotation variables are added specifically for each channel,
          i.e. prefixed with "greenSpecific_" and "redSpecific_". Do
          not use varLabels-names for subsetting.

     _p_D_a_t_a_S_l_i_d_e (exprSetRG): Returns an 'pData' object, i.e.
          'pData(phenoDataSlide(exprSetRG))'; cf. 'phenoDataSlide'. Do
          not use varLabels-names for subsetting.

     _p_h_e_n_o_D_a_t_a_G_r_e_e_n (exprSetRG): Returns an 'phenoData' object of the
          annotation information given for the green channel. Do not
          use varLabels-names for subsetting.

     _p_D_a_t_a_G_r_e_e_n (exprSetRG): Returns the 'pData' object taken out of
          the result of calling 'phenoDataGreen'. Do not use
          varLabels-names for subsetting.

     _p_h_e_n_o_D_a_t_a_R_e_d (exprSetRG): Returns an 'phenoData' object of the
          annotation information given for the red channel. Do not use
          varLabels-names for subsetting.

     _p_D_a_t_a_R_e_d (exprSetRG): Returns the 'pData' object taken out of the
          result of calling 'phenoDataRed'. Do not use varLabels-names
          for subsetting.

     _s_l_i_d_e_S_u_b_s_e_t (exprSetRG,i,j): Subsetting operation; where i
          corresponds to the rows  and j corresponds to the microarray
          slides. j is given by indexes or logicals related to the
          order of the channel pairs in 'channels'; cf. the constructor
          slot 'channels'.

     _g_e_t_I_n_d_G_r_e_e_n (exprSetRG): An accessor function for slot 'indGreen'.
          The corresponding elements of indGreen and indRed define
          microarray slides.

     _g_e_t_I_n_d_R_e_d (exprSetRG): An accessor function for slot 'indRed'. The
          corresponding elements of indGreen and indRed define
          microarray slides.

     [ (exprSetRG,i,j,type): A subset operator. Ensures that both the
          data and the annotation information ('phenoData') are
          subseted properly. This may only mix up the pairing of the
          channels, i.e. the validity of an exprSetRG, if you use
          argument option type == "invalidExprSetRG". Default:
          "validExprSetRG".

     _c_b_i_n_d (...): Concatenates 'exprSetRG' objects. Genes (rows) are
          assumed to match; cf. 'cbind.exprSetRG' 

     _a_s._e_x_p_r_S_e_t (exprSetRG): Class cast, returns an object of
          'exprSet', the information on the red and green channesl is
          discarded.

_A_u_t_h_o_r(_s):

     Andreas Buness <a.buness@dkfz.de>

_S_e_e _A_l_s_o:

     'exprSet-class', 'arrayData-class'

_E_x_a_m_p_l_e_s:

       indGreen=1:3
       indRed=4:6
       channels <- matrix( c(indGreen,indRed), nrow=length(indGreen), byrow=FALSE )
       colnames(channels) <- c("green","red")
       eSA <- new("exprSetRG", exprs=matrix(1:60, ncol=6, nrow=10), phenoData=
               new("phenoData", pData=data.frame(matrix(0,nrow=6,ncol=1)),
                   varLabels=list(rep("varLabel1",1))), channels=channels)
       stopifnot( all(pDataSlide(eSA) ==pData(eSA)[1:3,,drop=FALSE]) )
       eSAGreen <- getExprSetGreen(eSA)
       eSARed <- getExprSetRed(eSA)
       eSALogRatio <- getExprSetLogRatio(eSA)
       eSALogRatio2 <- getExprSetGreenMinusRed(eSA)
       eSALogRatio3 <- getExprSetRedMinusGreen(eSA)
       stopifnot( identical( eSALogRatio, eSALogRatio2 ) )
       stopifnot( identical( exprs(eSALogRatio), exprs(eSAGreen)-exprs(eSARed)) )
       stopifnot( all.equal.numeric( exprs(eSALogRatio3), exprs(eSARed)-exprs(eSAGreen)) )
       eSAPart <- eSA[,c(1,3,1,4,6,4)]
       eSAInvalid <- eSA[,c(1,3,1,5,6,4),type="invalidExprSetRG"]
       eSAPart2 <- slideSubset(eSA,j=c(1,3,1))

       eSAeSA <- cbind(eSA, eSA)
       eSAeSAPart2 <- cbind(eSA, eSAPart2)
       stopifnot(is(as.exprSet(eSA), "exprSet"))
       
      

